[gmx-users] Correct use of gmx traj -mol ?

Dallas Warren dallas.warren at monash.edu
Tue Nov 6 03:09:39 CET 2018


Have you tried the following?  I interpret that to mean that the index
fill will contain a group like this:

[ Molecules ]
i1 i2 i3 i4 i5 i6 ….. in

Where each i term corresponds to a particular molecule within the
system, and that number i will match up with the residue numbers.  So
can either make that by hand, that there should be also a method via
make_ndx to output the residue numbers into a group too.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Tue, 6 Nov 2018 at 12:12, James <james at ryley.com> wrote:
> Hi,
> I am interested in obtaining temperature readings that are corrected for
> velocity (meaning, if a molecule has a net velocity, that kinetic energy
> should not be counted as part of temperature). I suspect this is what the
> traj -mol option would do, but I can't get it to run without error.
> I am guessing the problem lies with my index files. The traj docs state
> that "When -mol is set, the numbers in the index file are interpreted as
> molecule numbers...". I don't understand this. All my index files contain
> are group headings and atom numbers. It seems like there would need to be
> another column that indicates molecule number (and I know such a column
> exists in some other file formats, but nothing I've read indicates that
> .ndx files can have extra columns).
> Any idea what I am doing wrong, or can anyone provide a set of test file on
> which "gmx traj -mol" can be successfully run?
> Sincerely,
> James
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